"But huge fee increases and Government cuts are leading to job losses and a lack of resources that is leaving the service struggling.

"The Government must think again about the new fees, which will plunge thousands of young people into serious debt. We know there is an alternative to fee hikes and service cuts."

Sally Hunt, general secretary of the University and College Union, said: "The Government's fee regime is in complete disarray and its sums clearly do not add up.

"It quickly became clear that all English universities would have to charge more than £6,000 a year just to break even, following devastating funding cuts.”

But David Willetts, the Universities Minister, said: "Our student and university finance reforms are fairer than the present system and affordable for the nation.

"No one will be asked to pay upfront costs, there will be more financial support for poorer students and funding for universities will follow individual study choices leading to an increased focus on graduate outcomes.

"Some universities have said they would like to charge £9,000 for some of their students but they have also proposed extensive fee waivers, while others have said they will charge significantly lower amounts.

"This means many students will pay less than the published price, and will subsequently borrow less."

Under the Government’s reforms, almost all direct state funding for university teaching is slashed and universities can charge up to £9,000 to plug the gap.

Any university wishing to charge more than £6,000 was supposed to submit an “access agreement” to Offa by Tuesday evening – outlining how they plan to admit poor teenagers.

It has been suggested that top universities should spend £1,000 out of every £9,000 received in fees on bursaries and outreach programmes for the most deprived students.

Figures suggest around 70 universities published fee levels by mid-afternoon on Tuesday, with 46 setting flat-rate £9,000 fees. A further six set fees at £9,000 for some courses.

Paul Jagger, chairman of Bradford University’s ruling council, said: “The decision to charge a fee of £9,000 is one that has been made with great reluctance but is set against the context of the devastating cuts to the sector and was reached after considerable discussion and consultation within the university.”

Offa said it would judge proposals by mid-July. Universities failing to meet Tuesday's deadline may have to wait longer for fee approval.

The watchdog has the power to prevent universities charging more than £6,000 if they fail to offer generous bursaries or outreach packages.